Re: Rise in Total Energy in NVE

From: S.K. Ghosh (skg30_at_cam.ac.uk)
Date: Thu Jul 10 2008 - 06:30:40 CDT

Hi NAMD users,

Thanks to Chris for his suggestion.

And is use of water sphere OK? I am aware that for a water sphere I am
using an artificial surface tension and also not using long range
electrostatics, but, should the values of force for unbinding vary for
these two cases (sphere vs box) - given that I am using a 15A padding for a
protein of radius 35A?

Could someone please comment and/or point to some literature/discussion on
justificatons of use of water sphere vs water box.

Thanks,
Sourav

On Jul 10 2008, Chris Harrison wrote:

>Sourav,
>1 fs should be adequate. If significant drift continues to occur, you
>might attempt 0.5fs to see if it decreases drift, but 1fs should be
>sufficient.
>
>-Chris
>
>
>On Wed, Jul 9, 2008 at 12:33 PM, S.K. Ghosh <skg30_at_cam.ac.uk> wrote:
>> Peter,
>>
>> Thanks for your suggestion. Is 1 fs OK to work with non-rigidbonds? or
>> would 0.5 fs be more appropriate?
>>
>> Thanks,
>> Sourav
>>
>> On Jul 9 2008, Peter Freddolino wrote:
>>
>>> Hi Sourav,
>>> spherical boundary conditions do work on the system (since they're
>>> applying forces). A rise in energy should not be surprising.
>>> Also, you may need to avoid multiple time stepping (ie, change
>>> fullElectFrequency to 1) to get perfect energy conservation.
>>>
>>> Peter
>>>
>>> S.K. Ghosh wrote:
>>>>
>>>> Hi Peter,
>>>>
>>>> I am now sending this to the group.
>>>>
>>>> Hi All,
>>>>
>>>> I find the total energy rising in an NVE run:
>>>>
>>>> First I ran an NVT (1 fs timestep and rigidbonds off) and then an NVE
>>>> (again 1 fs timestep and rigidbonds off) starting from where the NVT
>>>> run ended. For this NVE run, I find that the Total Energy is slightly
>>>> increasing initially (steady rise but approx 30 kcal/mol in total) for
>>>> 1 ns and looks to be almost flat for the last 1 ns (please find
>>>> attached). The temperature, however, does not rise at all.
>>>>
>>>> I am curious to find out why the energy rises. Could someone comment
>>>> on that please. Is 1 fs timestep high with rigidbonds turned off?
>>>> Should I use 0.5 fs?
>>>>
>>>> Or is this because of the following multistepping that I am using.
>>>>
>>>> timestep 1
>>>> #rigidBonds all
>>>> nonbondedFreq 1
>>>> fullElectFrequency 2 stepspercycle 10
>>>>
>>>> I have attached the energy values for 1st and last timestep here. I
>>>> can see that DIHED, IMPRP and ELECT have increased and VDW and
>>>> BOUNDARY have decreased.
>>>>
>>>> In both the runs, I have used spherical boundary conditions.
>>>>
>>>> Your comments would be much appreciated.
>>>>
>>>> Thanks,
>>>> Sourav
>>>>
>>>>
>>>> On Jul 7 2008, Peter Freddolino wrote:
>>>>
>>>>> Hi Sourav, this kind of question is really better addressed to
>>>>> namd-l, so that other users can learn from your question (and search
>>>>> for it later). For this increase in total energy, what other
>>>>> simulation parameters (timestep, etc) are you using? Is the energy
>>>>> rise continuous or does it fluctuate? If you use 1 fs timesteps
>>>>> without multiple timestepping, you should conserve energy quite well
>>>>> over time. Peter
>>>>>
>>>>> S.K. Ghosh wrote:
>>>>>>
>>>>>> Hi Peter,
>>>>>>
>>>>>> Starting from where an NVT ended, I ran an NVE i.e. turned off the
>>>>>> constant temperature control (the pressure control was turned off
>>>>>> for both). I found that the temperature was pretty stable but the
>>>>>> Total Energy curve showed slight increase (around 30 kcal/mol).
>>>>>> There was no change in timestep or rigidbonds or any other
>>>>>> parameters between the two runs. Though the energy rise is
>>>>>> comparatively quite low, is this something normal? I would be
>>>>>> interested to know why the Total Energy rises even though I am
>>>>>> running an NVE run. Could you please comment on this.
>>>>>>
>>>>>> Thanks,
>>>>>> Sourav
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>
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